My Life In Sequences

Leighton Pritchard

My life in sequences

A confession

The single most important influence on my academic career

Informal education

Informal education

Formal Education

BSc Forensic & Analytical Chemistry (1992-1996)

  • Mostly chemistry (1yr industry), final year forensics
  • Final year honours project: proteins and computers
  • Sinclair Basic and Frontier: Elite II

Body Fluid Analysis (1996)

  • Glasgow Royal Infirmary

Making the switch

PhD (1996-1999)

  • Evolution of snake venom toxins
  • Neural network model of evolution
  • Drug active site discovery algorithm (still in use)

doi:10.1006/jmbi.1998.2437; doi:10.1006/jtbi.1999.1043; PMID:11579223; PMID:12676977

First steps in academia

First steps in academia

Postdocs (1999-2003)

  • Systems biology: modelling yeast metabolism
  • Directed evolution: improved lanthanide binding

doi:10.1046/j.1432-1033.2002.03055.x; doi:10.1016/j.jtbi.2004.12.005

Multidisciplinarity

The SCRI/JHI Years

The SCRI/JHI Years


Bioinformatician (2003-present)

  • Research Institute
  • Government funding, policy remits
  • Ineligible for many usual funding sources (e.g. RCUK)
  • Bioinformatician/Computational Biologist
  • Not a clear postdoc/PI distinction
  • BA Mathematics (Open University)

Bacterial Genomics I

2003: Erwinia

  • Arrived at SCRI part-way through sequencing Erwinia carotovora subsp. atrosepticum

(http://sulab.org/2013/06/sequenced-genomes‐per‐year/)

Global pathogens

  • Blackleg, stem-rot
  • Quarantine pathogens

First enterobacterial plant pathogen genome

doi:10.1073/pnas.0402424101

Acceptable in the 00s…

  • 32-author single bacterial genome paper!
  • £250,000 collaboration between SCRI, University of Cambridge, Wellcome Trust Sanger Institute
  • All repeats and gaps bridged and sequenced directly
  • A single complete high-quality 5Mbp circular chromosome
  • 3 person-years’ manual annotation

TIL: Annotation

  • The utility of genomes depends on annotation
  • Annotation is curation, not cataloguing
  • Automated annotation from curated data (e.g. with Prokka) is the only game in town
  • But you can’t propagate what doesn’t exist
  • Lots of genomes, few incentives to curate well: “many parents, but no-one wants to look after the children”
  • ELIXIR, Ensembl, centralised resources only a partial solution

TIL: Comparisons

  • The real power of genomics is comparative genomics
  • \(\textrm{genome} \implies \textrm{heritable}\)
  • identification of functional elements, evolutionary processes and constraints
  • But epigenetics, tissue differentiation, mesoscale, phenotype plasticity, …

Comparisons

  • So we compared Pba to the 130 available bacterial genomes…

doi:10.1146/annurev.phyto.44.070505.143444

Functional differences

  • Pba-only: pathogenicity determinants; phage/IS elements
  • Pba & environmental: pathogenicity determinants; surface proteins; regulatory proteins

Visualisation

Visualisation

GenomeDiagram


doi:10.1093/bioinformatics/btk021

Biopython/KGML


http://biopython.org

Art/Science

  • Elaine Shemilt, exhibited Singapore, Dundee, London (2006)

A Blueprint for Bacterial Life and Art

Bacterial Genomics II

Bacterial genomics II

SPI-7 & cfa

  • 11 horizontally-acquired islands: one similar to a P. syringae phytotoxin synthesis island

SPI-7 & cfa

  • Island present in Pba, some Pcc, no Dickeya
  • cfl and cfa7 knockouts showed reduced virulence (17dpi)

Conclusions

As much as I know…

  • Do work you enjoy
  • Do it well
  • Work with good people
  • Read widely